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Yorodumi- PDB-1nrs: CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN R... -
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-Basic information
Entry | Database: PDB / ID: 1nrs | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / RECEPTOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / serine-type endopeptidase inhibitor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / positive regulation of cell growth / regulation of cell shape / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Tulinsky, A. / Mathews, I.I. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes. Authors: Mathews, I.I. / Padmanabhan, K.P. / Ganesh, V. / Tulinsky, A. / Ishii, M. / Chen, J. / Turck, C.W. / Coughlin, S.R. / Fenton 2nd., J.W. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Structure of the Hirudin-Thrombin Complex Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nrs.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nrs.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nrs_validation.pdf.gz | 403 KB | Display | wwPDB validaton report |
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Full document | 1nrs_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 1nrs_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 1nrs_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/1nrs ftp://data.pdbj.org/pub/pdb/validation_reports/nr/1nrs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO H 37 2: A FEW SIDE CHAINS IN BOTH THROMBIN AND RECEPTOR PEPTIDE DO NOT HAVE WELL-DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.01 IN THIS ENTRY. | |||||||||
Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734, thrombin | ||
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734, thrombin | ||
#3: Protein/peptide | Mass: 500.569 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CLEAVED, FIRST FOUR RESIDUES ONLY / Source: (gene. exp.) Homo sapiens (human) | ||
#4: Protein/peptide | Mass: 1534.554 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945 | ||
#5: Water | ChemComp-HOH / | ||
Compound details | THE CLEAVED RECEPTOR FRAGMENT LDPR (CHAIN R) IS BOUND IN THE ACTIVE SITE IN A PRODUCTIVESequence details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR HIRUGEN. CHAIN INDICATOR *R* IS USED FOR CLEAVED NRP. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % | |||||||||||||||
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Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.4 Å / % possible obs: 85 % / Rmerge F obs: 0.029 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.4→7 Å / σ(F): 2 Details: A FEW SIDE CHAINS IN BOTH THROMBIN AND RECEPTOR PEPTIDE DO NOT HAVE WELL-DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN GIVEN OCCUPANCIES OF 0.01 IN THIS ENTRY.
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Refinement step | Cycle: LAST / Resolution: 2.4→7 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26 Å2 |